3 Answers
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IPv6 over the VPNs in NetworkManager is not currently supported in 12.04 and prior releases of Ubuntu. It is a new feature introduced in a further release of NetworkManager (0.9.6.0), so it will be available, to begin with, on the OpenConnect plugin only. Such support will be available in Quantal Quetzal (Ubuntu 12.10).

OpenVPN and the like do an IPv4 tunnel but don't handle IPv6 which has an entirely different stack. If you have a /48 or /56 IPv6 allocation you can create a /64 network and use and 6to4 tunnel to connect over the VPN.

Use native IPv6 roaming. You will want to enable IPSec for your IPv6 network if you do this. The roaming server will need an IPv6 address where it is. It then notifies your IPv6 router where to route its traffic. This is designed to handle individual systems like laptops. At a minimum, the headers should be secured with IPv6.

@singpolyma: I don't think they are here yet, and I hope the never are. Support for encrypted remote access is built into the IPv6 protocol. I think open-source efforts would be better spent providing GUI solutions to support IPv6 native tunneling. I have seen a posting for adding an IPv6 addresses and route to an OpenVPN tunnel. It appears OpenVPN supports tunneling IPv6 in TAP mode.
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BillThor Mar 10 '11 at 14:24